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- PDB-6izr: Whole structure of a 15-stranded ParM filament from Clostridium b... -

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Basic information

Entry
Database: PDB / ID: 6izr
TitleWhole structure of a 15-stranded ParM filament from Clostridium botulinum
ComponentsPutative plasmid segregation protein ParM
KeywordsPROTEIN FIBRIL / ParM / filaments / cytoskeleton
Function / homologyActin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / ADENOSINE-5'-DIPHOSPHATE / Actin-like protein N-terminal domain-containing protein
Function and homology information
Biological speciesClostridium botulinum Prevot_594 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsKoh, F. / Narita, A. / Lee, L.J. / Tan, Y.Z. / Dandey, V.P. / Tanaka, K. / Popp, D. / Robinson, R.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privateSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateF00316 United States
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a 15-stranded actin-like filament from Clostridium botulinum.
Authors: Fujiet Koh / Akihiro Narita / Lin Jie Lee / Kotaro Tanaka / Yong Zi Tan / Venkata P Dandey / David Popp / Robert C Robinson /
Abstract: Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein ...Microfilaments (actin) and microtubules represent the extremes in eukaryotic cytoskeleton cross-sectional dimensions, raising the question of whether filament architectures are limited by protein fold. Here, we report the cryoelectron microscopy structure of a complex filament formed from 15 protofilaments of an actin-like protein. This actin-like ParM is encoded on the large pCBH Clostridium botulinum plasmid. In cross-section, the ~26 nm diameter filament comprises a central helical protofilament surrounded by intermediate and outer layers of six and eight twisted protofilaments, respectively. Alternating polarity of the layers allows for similar lateral contacts between each layer. This filament design is stiffer than the actin filament, and has likely been selected for during evolution to move large cargos. The comparable sizes of microtubule and pCBH ParM filaments indicate that larger filament architectures are not limited by the protomer fold. Instead, function appears to have been the evolutionary driving force to produce broad, complex filaments.
History
DepositionDec 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
1: Putative plasmid segregation protein ParM
2: Putative plasmid segregation protein ParM
A: Putative plasmid segregation protein ParM
B: Putative plasmid segregation protein ParM
D: Putative plasmid segregation protein ParM
E: Putative plasmid segregation protein ParM
G: Putative plasmid segregation protein ParM
H: Putative plasmid segregation protein ParM
J: Putative plasmid segregation protein ParM
K: Putative plasmid segregation protein ParM
M: Putative plasmid segregation protein ParM
N: Putative plasmid segregation protein ParM
P: Putative plasmid segregation protein ParM
Q: Putative plasmid segregation protein ParM
b: Putative plasmid segregation protein ParM
c: Putative plasmid segregation protein ParM
e: Putative plasmid segregation protein ParM
f: Putative plasmid segregation protein ParM
h: Putative plasmid segregation protein ParM
i: Putative plasmid segregation protein ParM
k: Putative plasmid segregation protein ParM
l: Putative plasmid segregation protein ParM
n: Putative plasmid segregation protein ParM
o: Putative plasmid segregation protein ParM
q: Putative plasmid segregation protein ParM
r: Putative plasmid segregation protein ParM
t: Putative plasmid segregation protein ParM
u: Putative plasmid segregation protein ParM
w: Putative plasmid segregation protein ParM
x: Putative plasmid segregation protein ParM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,200,35090
Polymers1,186,80530
Non-polymers13,54560
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area76540 Å2
ΔGint-689 kcal/mol
Surface area462730 Å2

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Components

#1: Protein ...
Putative plasmid segregation protein ParM


Mass: 39560.168 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum Prevot_594 (bacteria)
Gene: T258_3831 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4W229
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ParM filament coded on pCBH plasmid from Clostridium botulinum
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridium botulinum F str. 230613 (bacteria) / Organelle: pCBH plasmid
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET-21d
Buffer solutionpH: 7.4
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -50.37 ° / Axial rise/subunit: 50.26 Å / Axial symmetry: C1
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33356 / Symmetry type: HELICAL

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